Johnson Steven M, Tan Frederick J, McCullough Heather L, Riordan Daniel P, Fire Andrew Z
Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5324, USA.
Genome Res. 2006 Dec;16(12):1505-16. doi: 10.1101/gr.5560806. Epub 2006 Oct 12.
Nucleosome positions within the chromatin landscape are known to serve as a major determinant of DNA accessibility to transcription factors and other interacting components. To delineate nucleosomal patterns in a model genetic organism, Caenorhabditis elegans, we have carried out a genome-wide analysis in which DNA fragments corresponding to nucleosome cores were liberated using an enzyme (micrococcal nuclease) with a strong preference for cleavage in non-nucleosomal regions. Sequence analysis of 284,091 putative nucleosome cores obtained in this manner from a mixed-stage population of C. elegans reveals a combined picture of flexibility and constraint in nucleosome positioning. As has previously been observed in studies of individual loci in diverse biological systems, we observe areas in the genome where nucleosomes can adopt a wide variety of positions in a given region, areas with little or no nucleosome coverage, and areas where nucleosomes reproducibly adopt a specific positional pattern. In addition to illuminating numerous aspects of chromatin structure for C. elegans, this analysis provides a reference from which to begin an investigation of relationships between the nucleosomal pattern, chromosomal architecture, and lineage-based gene activity on a genome-wide scale.
染色质景观中的核小体位置是DNA对转录因子和其他相互作用成分可及性的主要决定因素。为了描绘模式遗传生物秀丽隐杆线虫中的核小体模式，我们进行了全基因组分析，其中使用一种对非核小体区域的切割有强烈偏好的酶（微球菌核酸酶）释放与核小体核心相对应的DNA片段。以这种方式从秀丽隐杆线虫的混合发育阶段群体中获得的284,091个推定核小体核心的序列分析揭示了核小体定位中灵活性和限制性的综合情况。正如先前在不同生物系统中对单个基因座的研究所观察到的那样，我们在基因组中观察到这样一些区域：在给定区域内核小体可以采用多种位置；几乎没有或没有核小体覆盖的区域；以及核小体可重复采用特定位置模式的区域。除了阐明秀丽隐杆线虫染色质结构的众多方面之外，该分析还提供了一个参考，以便在全基因组范围内开始研究核小体模式、染色体结构和基于谱系的基因活性之间的关系。
